#class05 R graphics intro
# My first boxplot
x<-rnorm(1000,0)
boxplot(x)
summary(x)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## -2.972810 -0.619080 0.016524 0.004789 0.677037 3.254438
hist(x)
boxplot(x, horizontal = TRUE)
#Line plot
weight <- read.table("bimm143_05_rstats/weight_chart.txt", header=TRUE)
plot(weight$Age, weight$Weight, type = "o",
pch=15, cex=1.5, lwd=2, ylim=c(2,10), xlab = "Age (months)",
ylab="Weight (kg)", main="Baby Weight with Age")
#Barplot
mouse<- read.table("bimm143_05_rstats/feature_counts.txt", sep="\t", header=TRUE)
barplot(mouse$Count)
par(mar=c(3.1, 11.1, 4.1, 2))
barplot(mouse$Count, names.arg=mouse$Feature,
horiz=TRUE, ylab="",
main="Number of features in the mouse GRCm38 genome",
las=1, xlim=c(0,80000))
#Histogram
x<-c(rnorm(1000), rnorm(1000)+4)
hist(x, breaks=80)
par( mar=c(5, 4, 1, 1) )
#providing color vectors
mf <- read.delim("bimm143_05_rstats/male_female_counts.txt")
barplot(mf$Count,names.arg=mf$Sample, col=rainbow(nrow(mf)),
las=2, ylab="Counts")
barplot(mf$Count,names.arg=mf$Sample, col=c("blue", "red"),
las=2, ylab="Counts")
#Coloring by value
genes<-read.delim("bimm143_05_rstats/up_down_expression.txt")
table(genes$State)
##
## down unchanging up
## 72 4997 127
palette(c("blue", "gray", "red"))
plot(genes$Condition1, genes$Condition2, col=genes$State, xlab="Expression condition 1", ylab="Expression condition 2")
#Dynamic use of color
meth<-read.delim("bimm143_05_rstats/expression_methylation.txt")
dcols<-densCols(meth$gene.meth, meth$expression)
plot(meth$gene, meth$expression,col=dcols, pch=20)
inds <- meth$expression > 0
plot(meth$gene.meth[inds], meth$expression[inds])
dcols <- densCols(meth$gene.meth[inds], meth$expression[inds])
plot(meth$gene.meth[inds], meth$expression[inds], col = dcols, pch = 20)
dcols.custom <- densCols(meth$gene.meth[inds], meth$expression[inds],
colramp = colorRampPalette(c("blue2",
"green2",
"red2",
"yellow")) )
plot(meth$gene.meth[inds], meth$expression[inds],
col = dcols.custom, pch = 20)
